An accurate characterization of the fine molecular structure of starch in terms of the chain length distribution (CLD) of amylopectin requires complete dispersion of the starch in a solvent, either buffer or water and the non-interference of this on the subsequent enzymatic debranching of starch with isoamylase (pretreatments before determining the CLD). In this study, the HYLON V and HYLON VII starches (commercial high-amylose corn starches) were selected, since high-amylose starches typically present difficulties in their dispersion and, therefore, the study of their fine structure can commonly present errors. The goal of this research was to study two water dispersion treatments (1. boiling water for 1 h and 2. autoclaving at 120 °C and 15 Psi for 15 min) to achieve a fast and reliable method of the fine structure of two high-amylose corn starches using high-performance size exclusion chromatography coupled with a refractive index detector (HPSEC-RID) and high-performance anion-exchange chromatography coupled a pulsed amperometric detector (HPAEC-PAD). The HPSEC-RID chromatograms of both starches showed better resolution using autoclaving than boiling water treatment. The two starches tested had higher amylose and degree of polymerization (DP) values utilizing the autoclaving than the boiling water treatment. However, no appreciable differences were observed in the CLD values employing HPAEC-PAD for either of the two water dispersion treatments. Lastly, the water dispersion treatment by autoclaving before enzymatic debranching is recommended to obtain a more accurate quantification of the amylose content of high-amylose starches.